Treat with loperamide at 5 dpf for 24 hours.
At each timepoint:
For individual strains:
Make 0 to -3 dilutions in 96-well plates, in triplicate (8 fish per
plate)
Plate 10 µL microdrops on big square plates.
8 square plates total per timepoint
Put plates at 28C for 2 days, then count colonies.
# import individual strain data
datacfustrial49<-
readxl::read_xlsx("../Trial49_LoperamideCFUs/Trial49_LoperamideZebrafishWaterCFUs.xlsx", sheet="Fish") %>%
drop_na(DF) %>%
mutate(LoperamideTreatment=factor(LoperamideTreatment,
levels=c("None", "DMSO", "Loperamide 10 mg/L"),
labels=c("Control","DMSO", "Loperamide")),
Treatment = factor(Treatment,
levels=c("Bc1","Bc2","Bc3","Bc4","Bc10","Bc1/Bc2/Bc3/Bc4/Bc10")),
Timepoint = case_when(TrialDay == "6" ~ "24 hr treatment",
TrialDay == "7" ~ "Treatment +\n24 hr recovery",
TrialDay == "11" ~ "Treatment +\n5 day recovery"),
Timepoint_day = case_when(TrialDay == "6" ~ "T0",
TrialDay == "7" ~ "T1",
TrialDay == "11" ~ "T5"))
# import individual strain data
datacfustrial56 <-
readxl::read_xlsx("../Trial56_LoperamideMonoCFUs/Trial56_LoperamideZebrafishMonoCFUs.xlsx", sheet="Fish") %>%
drop_na(DF) %>%
mutate(LoperamideTreatment=factor(LoperamideTreatment,
levels=c("None", "DMSO", "Loperamide 10 mg/L"),
labels=c("Control","DMSO", "Loperamide")),
Treatment = factor(Treatment,
levels=c("W6. Variovorax", "W8. Rhizobium sp.", "Mz8. Ochrobactrum"),
labels=c("W6","W8","Mz8")),
Timepoint = case_when(TrialDay == "6" ~ "24 hr treatment",
TrialDay == "7" ~ "Treatment +\n24 hr recovery",
TrialDay == "11" ~ "Treatment +\n5 day recovery"),
Timepoint_day = case_when(TrialDay == "6" ~ "T0",
TrialDay == "7" ~ "T1",
TrialDay == "11" ~ "T5"))
# import individual strain data
datacfustrial57 <-
readxl::read_xlsx("../Trial57_LoperamideMonoMixCFUs/Trial57_LoperamideZebrafishMixMonoCFUs.xlsx", sheet="FishMono") %>%
drop_na(DF) %>%
mutate(LoperamideTreatment=factor(LoperamideTreatment,
levels=c("None", "DMSO", "Loperamide 10 mg/L"),
labels=c("Control","DMSO", "Loperamide")),
Treatment = factor(Treatment,
levels=c("Mz1. Achromobacter","F. johnsoniae"),
labels=c("Mz1","Fjohn")),
Timepoint = case_when(TrialDay == "6" ~ "24 hr treatment",
TrialDay == "7" ~ "Treatment +\n24 hr recovery",
TrialDay == "11" ~ "Treatment +\n5 day recovery"),
Timepoint_day = case_when(TrialDay == "6" ~ "T0",
TrialDay == "7" ~ "T1",
TrialDay == "11" ~ "T5"))
straininfo <- readxl::read_xlsx("../../LoperamideStrainInfo.xlsx") %>%
mutate(Strain=recode(Strain, "W6t"="W6"))
dataall <- full_join(datacfustrial49,datacfustrial56) %>% full_join(datacfustrial57) %>%
left_join(straininfo, by=c("Treatment"="Strain")) %>%
mutate(CodeName=factor(CodeName, levels=unique(straininfo$CodeName)))
| Treatment | Timepoint | Timepoint_day | CodeName | .y. | group1 | group2 | p | p.adj | p.format | p.signif | method |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Bc1 | 24 hr treatment | T0 | S7. *Aeromonas veronii 1* | CFUs_perFish | DMSO | Loperamide | 0.04206641 | 1 | 0.042 | * | Wilcoxon |
| Bc2 | 24 hr treatment | T0 | S1. *Pseudomonas mossellii* | CFUs_perFish | DMSO | Loperamide | 0.02857143 | 1 | 0.029 | * | Wilcoxon |
| Bc2 | Treatment + 24 hr recovery | T1 | S1. *Pseudomonas mossellii* | CFUs_perFish | DMSO | Loperamide | 0.02857143 | 1 | 0.029 | * | Wilcoxon |
| Bc1 | Treatment + 5 day recovery | T5 | S7. *Aeromonas veronii 1* | CFUs_perFish | DMSO | Loperamide | 0.02940105 | 1 | 0.029 | * | Wilcoxon |
| Mz8 | 24 hr treatment | T0 | S9. *Ochrobactrum tritici* | CFUs_perFish | DMSO | Loperamide | 0.02857143 | 1 | 0.029 | * | Wilcoxon |
| W8 | Treatment + 5 day recovery | T5 | S8. *Rhizobium sp.* | CFUs_perFish | DMSO | Loperamide | 0.02857143 | 1 | 0.029 | * | Wilcoxon |
| Fjohn | 24 hr treatment | T0 | S10. *Flavobacterium johnsoniae* | CFUs_perFish | DMSO | Loperamide | 0.02842954 | 1 | 0.028 | * | Wilcoxon |
| Fjohn | Treatment + 24 hr recovery | T1 | S10. *Flavobacterium johnsoniae* | CFUs_perFish | DMSO | Loperamide | 0.02940105 | 1 | 0.029 | * | Wilcoxon |
Stats are relative to DMSO